Merge branch 'develop' into features/JAL-3010ontologyFeatureSettings

[jalview.git] / src / jalview / gui / CrossRefAction.java

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 21a0a84..7045481 100644 (file)
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -143,7 +143,7 @@ public class CrossRefAction implements Runnable
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       if (Cache.getDefault("HIDE_INTRONS", true))
       {
-        newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
+        newFrame.hideFeatureColumns(false, SequenceOntologyI.EXON);
       }
       String newtitle = String.format("%s %s %s",
               dna ? MessageManager.getString("label.proteins")
@@ -176,10 +176,14 @@ public class CrossRefAction implements Runnable
       /*
        * copy feature rendering settings to split frame
        */
-      newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
-              .transferSettings(myFeatureStyling);
-      copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
-              .transferSettings(myFeatureStyling);
+      FeatureRenderer fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
+              .getFeatureRenderer();
+      fr1.transferSettings(myFeatureStyling);
+      fr1.findAllFeatures(true);
+      FeatureRenderer fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
+              .getFeatureRenderer();
+      fr2.transferSettings(myFeatureStyling);
+      fr2.findAllFeatures(true);
 
       /*
        * apply 'database source' feature configuration
@@ -336,7 +340,7 @@ public class CrossRefAction implements Runnable
 
     /*
      * hack: ignore cross-references to Ensembl protein ids
-     * (can't fetch chromosomal mapping for these)
+     * (or use map/translation perhaps?)
      * todo: is there an equivalent in EnsemblGenomes?
      */
     if (accession.startsWith("ENSP"))